Chemical Engineering Seminar

Title: Mechanical Interactions and Growth Dynamics of Bacterial Colonies in Constrained Environments

Abstract: Understanding how microorganisms organize, adapt, and survive in physically constrained environments is fundamental to both microbiology and ecosystem science. Initially, we investigated the self-organization of non-motile rod-shaped bacteria confined to two-dimensional surfaces. Using molecular dynamics simulations, we demonstrated that growth-generated mechanical forces, modulated by bacterial interactions, confinement geometry, and environmental mechanical properties, can lead to emergent colony-level alignment and structural order. These results highlight the role of mechanical feedback in driving spatial patterning and adaptive dynamics in microbial systems. Next, we extended this model into three dimensions by introducing isotropic pressure as a form of soft confinement. This required adapting the 2D simulation framework to handle contact mechanics in dense, stress-responsive 3D environments. While this work is ongoing, it lays essential groundwork for understanding how mechanical constraints influence population-scale dynamics in more realistic geometries. Finally, we are beginning to explore a broader systems-level perspective by developing a network-based model of microbial interactions in structured soils under environmental stress. Though still in early stages, this direction reflects a shift toward connecting microscale mechanics with ecological resilience in the face of climate extremes.

Biography: Samaneh Rahbar is a postdoctoral researcher in the Department of Physics and Astronomy at the University of California, Riverside. She received her Ph.D. in Physics from Saarland University in Germany. Her research lies at the intersection of soft matter physics, computational biophysics, and microbial ecology, with a particular focus on how mechanical forces and spatial constraints shape the growth and organization of microbial communities. Using molecular dynamics simulations and network-based models, she investigates the emergence of collective behavior in bacterial colonies under physical confinement, as well as the resilience of microbial networks in environmentally stressed soils. Her work bridges microscale biophysical mechanisms and macroscale ecological dynamics, reflecting a broader goal of understanding microbial life across physical and environmental scales.